The GLI for AMD64 appears to be placing ACCEPT_KEYWORDS="~x86" in make.conf instead of the correct value of ~amd64 when using the ~arch checkbox.
*** Bug 146554 has been marked as a duplicate of this bug. ***
Eh, I completely overlooked this when adding support for amd64.
As a workaround until this is fixed, editing the installprofile.xml to have ~amd64 as opposed to ~x86 should work. P.S. Sorry for the duplicate, my 1st time bug reporting :-)
Fixed in CVS.